From: Carsten Olbrich (c.olbrich_at_jacobs-university.de)
Date: Mon Jun 18 2007 - 11:04:30 CDT
Dear users,
I use the binaries from NAMD download side and apply tclfoces to my molecule.
When I'm using the 32bit binary on our cluster (quad core Intel Xeon
processors) the job runs fine.
But if I'm using the 64bit binary after some while (200000-1000000
steps) I get an error.
One time the error are "Atoms moving too fast", another time "Stray
PME grid charges detected!" or "Bad global exclusion count"....
The same things happen if I compile the binary myself.
Is there a way to work around or any idea for a reason?
Thanks for your help...
Carsten
A sample output:
Info: NAMD 2.6 for Linux-amd64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.6 Linux-amd64 24 node23 colbrich
Info: Running on 24 processors.
Info: 7612 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is Conf_pull_dna.conf
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE out_eq_xy_dna.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 68.2539 0 0
Info: PERIODIC CELL BASIS 2 0 165.76 0
Info: PERIODIC CELL BASIS 3 0 0 48.7528
Info: PERIODIC CELL CENTER 0 0 10
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: VELOCITY FILE out_eq_xy_dna.restart.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME out_pull_dna.dcd
Info: DCD FREQUENCY 5000
Info: DCD FIRST STEP 5000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME out_pull_dna.xst
Info: XST FREQUENCY 10000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME out_pull_dna
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME out_pull_dna.restart
Info: RESTART FREQUENCY 10000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 21
Info: ENERGY OUTPUT STEPS 5000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 5000
Info: TCL GLOBAL FORCES ACTIVE
Info: TCL GLOBAL FORCES SCRIPT Force_pull_dna.tcl
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 81 180 64
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1182151013
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB dna_xy.pdb
Info: STRUCTURE FILE dna_xy.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES out_eq_xy_dna.restart.coor
Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0
USING VALUES k=130 theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 299 BONDS
Info: 729 ANGLES
Info: 1145 DIHEDRAL
Info: 84 IMPROPER
Info: 0 CROSSTERM
Info: 161 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 55933 ATOMS
Info: 37689 BONDS
Info: 18164 ANGLES
Info: 0 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 167799 DEGREES OF FREEDOM
Info: 19143 HYDROGEN GROUPS
Info: TOTAL MASS = 344144 amu
Info: TOTAL CHARGE = 2.8424e-06 e
Info: *****************************
Info: Entering startup phase 0 with 21864 kB of memory in use.
Info: Entering startup phase 1 with 21864 kB of memory in use.
Info: Entering startup phase 2 with 30292 kB of memory in use.
Info: Entering startup phase 3 with 30292 kB of memory in use.
Info: PATCH GRID IS 3 (PERIODIC) BY 7 (PERIODIC) BY 2 (PERIODIC)
Info: REMOVING COM VELOCITY -0.0263814 0.0100015 0.00261442
Info: LARGEST PATCH (31) HAS 1460 ATOMS
Info: CREATING 9644 COMPUTE OBJECTS
Info: Entering startup phase 4 with 38448 kB of memory in use.
Info: PME using 21 and 23 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: Entering startup phase 5 with 38448 kB of memory in use.
Info: Entering startup phase 6 with 38448 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 38448 kB of memory in use.
Info: CREATING 9644 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: Entering startup phase 8 with 40012 kB of memory in use.
Info: Finished startup with 40012 kB of memory in use.
TCL: Running for 10000000 steps
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